[1] He won the 2009 Copa Simón Bolívar with Guabirá, and was in charge of Ciclón for a brief period in the following year, taking over the club in June and resigning in August.
[2] In January 2021, Peña was named in charge of Real Santa Cruz, and missed out promotion in the final stages of the 2012–13 Liga Nacional B.
In 2014, he was a part of his brother's staff at San José,[1] and both later started a football school in their hometown.
Peña returned to managerial duties in 2017, taking over another club he represented as a player, Destroyers.
[4] The following 14 March, he returned to the top tier after being named in charge of newcomers Libertad Gran Mamoré,[5] but was sacked on 20 July 2023.